Yes, it worked. Thank you. I had to use different pin numbering as @luz explained in this answer for my CAN bus question.

@György-Farkas My question is if i connect a switch only with 3,3V and an input GPIO, could i always read the correct input? That option is necessary to keep my cable management. Maybe its to be realized by using analog inputs with the arduino dock.

@György-Farkas said in newbie issue with gpioctl not seeing HIGH on Arduino Dock 2: ATmega chip That worked, thank you. However I have an OLED on the expansion header so I would prefer to use the ATmega pins because that is why I bought the Arduino Dock 2 board. I think I found the direction to flash the ATmega pins, however I don't see a sketch to program it with, or documentation on what commands to use to control those pins.